One good practice I would suggest (as what I have done with all the mods), is to have separated installations for each mods (GEM+ can easily switch between mods). While it will inevitably take more of hard disk space (for tracks mainly), it will be unlikely to run into trouble or mess up things, and far easier to find out what's gone wrong (and very easy to backup stuff for specific mod, just ZIP the dir and call it XX year mod).